Fig 1.
NRAP environmental microbiome metagenomic roadmap.
Photo inset: A. The NRAP Water Treatment Facility in Española, NM, USA. B. Interior showing the flow control system and tanks used for amendment mixing and injection. C. On-site e-biome concentration through a filter capsule. Quantitation using PCR (shown in red) a molecular biology tool (MBT) were used in 2006 to detect indigenous microbes capable of ERD. The detection of functional genes (shown in grey) is possible with gene-specific primers. Metagenomic tools (MGTs) involve the use of next generation sequencing (NGS) applied to whole metagenomes or to the pool of amplicons produced with universal primers.
Table 1.
NRAP shallow plume treatment and e-biome sampling history.
Fig 2.
Of 857 validly assigned genera (no Candidatus), 186 have documented O2 requirements. S5 File is an interactive htlm plot for PC 1 and 2 that is limited to genera with known O2 requirements. Domain-level annotations are indicated by marker shape Pointing at any marker in S5 File brings up a window that identifies the genus.
Fig 3.
Phylum and selected class-level abundances.
Cell plots are sorted from high to low abundance at baseline. WMS-U and 16S rRNA data are shown for six samples, including two samples for four- and 23-month sampling events. OHRG and COMG classification include only literature validated taxa (S2 and S3 Tables in S1 File).
Fig 4.
These genera increase in abundance at NRAP and have rdh-containing genomes in IMG/M. The red font indicates that rdh -containing scaffolds were detected at NRAP and asterisks indicate literature-validated OHRG (S1 Table in S1 File).
Fig 5.
The standard errors for the 16S rRNA gene amplicons are shown, but most are too small to be discernable. Note that the RPM range is greater in B than the other graphs.
Fig 6.
Strain-level OH respiration and abundance profiles.
Literature-validated OH-respiring strains combined with abundance profiles demonstrates the pathway for PCE degradation at NRAP. References for the OH-profiles are provided in S6 Table in S1 File.
Fig 7.
Representative scaffolds containing rdh gene clusters.
Scaffolds are the result of a combined assembly that includes reads from all timepoints and both wells. Details for all rdh-containing scaffolds are in S8 Table in S1 File.
Fig 8.
Methane levels are included since both methanogens and methanotrophs can modulate methane level. A. Methanogenic Archaea. Methanosarcina is not detected by 16S at baseline and Methanolobus is not detected by 16S at any timpoint. B. Genomes with mo genes in the IMG/M database and have the potential to oxidize TCE and includes methanotrophs Methylocystis and Methylosinus. Xanthobacter is not detected at baseline by 16S.
Fig 9.
These genera exhibit an increase in abundance in at least one sample after baseline. Red font indicates that the cld gene is detected in an NRAP scaffold. Bold font indicates that dark-O2 producing gene products (cld and/or nod) detected in other groundwater studies [31].
Fig 10.
NRAP sampling and sequencing overview.
The baseline (0 months) is shaded and all Y-axes are log10 values. A. Liters of water filtered on-site and biomass as measured by DNA yield from each sample. B. Sequencing depth and WMS-U identification. C. Sequencing depth and scaffold profiles for well SAE3 over time.
Fig 11.
Domain-level abundance and methane saturation.
WMS-U and 16S amplicons detected Archaea at baseline but methane was not detected until after the start of remediation.
Fig 12.
The NRAP model for successful ERD.
The goal of ERD is the complete respiration of OHs and the presence of Dhc195 and Dhb (in bold) determined by qPCR in 2006 indicated that biostimulation was the remedy of choice. The numbers shown in the respiration pathway indicate when each compound reached its peak in the first 3.25 yrs. of the project. Relevant microbes whose presence is supported by MGT are indicated in the number lists. 1. PCE and TCE respiring strains 2. DCE respiring strains. 3. VC respiring strains. 4. Microbes that harbor rdh genes but are not validated as OHRG. TCE can also be subjected to anaerobic or aerobic cometabolic processes. 5. Methanogenic Archaea. 6. Methanotrophs and other mo-containing microbes can oxidase TCE, eliminating the double bond and producing unstable epoxides. 7. Hydrolytic dehalogenases are abundant in the NRAP microbiome, including in microbes that play other roles in dechlorination. The potential for products produced by aerobic cometabolism, such as chlorinated ethanes, remain to be verified. 8. The O2 for aerobic cometabolism may be produced by microbes that harbor chlorite dismutase.